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Quantitative trait locus mapping of deep rooting by linkage and association analysis in rice.

Lou Q, Chen L, Mei H, Wei H, Feng F, Wang P, Xia H, Li T, Luo L - J. Exp. Bot. (2015)

Bottom Line: Forty-eight significant SNPs of the RDR were identified and formed a clear peak on the short arm of chromosome 1 in a Manhattan plot.Seven of the nine candidate SNPs identified by association mapping were verified in two RDR extreme groups.The findings from this study will be beneficial to rice drought-resistance research and breeding.

View Article: PubMed Central - PubMed

Affiliation: Shanghai Agrobiological Gene Center, No. 2901, Beidi Road, Minhang District, Shanghai 201106, PR China Fudan University, No. 220, Handan Road, Yangpu District, Shanghai 200433, PR China.

No MeSH data available.


Distribution of nine candidate SNPs in 20 extreme varieties from collection 3. The upper panel shows the results for the extreme shallow-rooting varieties (in italic), and the lower panel shows the extreme deep-rooting varieties. The average values of RDR from the shallow-rooting and deep-rooting groups are given (meansa and meansb, respectively). A red box indicates a major SNP allele type in the deep-rooting group, and a blue box represents another allele type of this SNP.
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Figure 5: Distribution of nine candidate SNPs in 20 extreme varieties from collection 3. The upper panel shows the results for the extreme shallow-rooting varieties (in italic), and the lower panel shows the extreme deep-rooting varieties. The average values of RDR from the shallow-rooting and deep-rooting groups are given (meansa and meansb, respectively). A red box indicates a major SNP allele type in the deep-rooting group, and a blue box represents another allele type of this SNP.

Mentions: Collection 3 contained 377 landraces that were used to determine the reliability of the candidate SNPs identified by the GWAS. Twenty landraces with extreme RDR values at the two opposite ends were chosen from this collection for candidate SNP verification. The average values of RDR were 49.4 and 14.4% in the extreme high and low groups, respectively. Nine candidate SNPs were randomly chosen for further verification. Through Sanger sequencing of the PCR products, we obtained sequence information on the candidate SNPs in the 20 RDR extreme landraces (Fig. 5, Supplementary Table S4, available at JXB online).


Quantitative trait locus mapping of deep rooting by linkage and association analysis in rice.

Lou Q, Chen L, Mei H, Wei H, Feng F, Wang P, Xia H, Li T, Luo L - J. Exp. Bot. (2015)

Distribution of nine candidate SNPs in 20 extreme varieties from collection 3. The upper panel shows the results for the extreme shallow-rooting varieties (in italic), and the lower panel shows the extreme deep-rooting varieties. The average values of RDR from the shallow-rooting and deep-rooting groups are given (meansa and meansb, respectively). A red box indicates a major SNP allele type in the deep-rooting group, and a blue box represents another allele type of this SNP.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4507776&req=5

Figure 5: Distribution of nine candidate SNPs in 20 extreme varieties from collection 3. The upper panel shows the results for the extreme shallow-rooting varieties (in italic), and the lower panel shows the extreme deep-rooting varieties. The average values of RDR from the shallow-rooting and deep-rooting groups are given (meansa and meansb, respectively). A red box indicates a major SNP allele type in the deep-rooting group, and a blue box represents another allele type of this SNP.
Mentions: Collection 3 contained 377 landraces that were used to determine the reliability of the candidate SNPs identified by the GWAS. Twenty landraces with extreme RDR values at the two opposite ends were chosen from this collection for candidate SNP verification. The average values of RDR were 49.4 and 14.4% in the extreme high and low groups, respectively. Nine candidate SNPs were randomly chosen for further verification. Through Sanger sequencing of the PCR products, we obtained sequence information on the candidate SNPs in the 20 RDR extreme landraces (Fig. 5, Supplementary Table S4, available at JXB online).

Bottom Line: Forty-eight significant SNPs of the RDR were identified and formed a clear peak on the short arm of chromosome 1 in a Manhattan plot.Seven of the nine candidate SNPs identified by association mapping were verified in two RDR extreme groups.The findings from this study will be beneficial to rice drought-resistance research and breeding.

View Article: PubMed Central - PubMed

Affiliation: Shanghai Agrobiological Gene Center, No. 2901, Beidi Road, Minhang District, Shanghai 201106, PR China Fudan University, No. 220, Handan Road, Yangpu District, Shanghai 200433, PR China.

No MeSH data available.